The reason I asked about the E-brake is that I suspect something related to the E-brake mechanism could be letting go or realigning when you first move backwards. If you stopped using the E-brake for a period, wonder if the noise goes away? I realize that does not solve the problem but it may help focus on the root cause.
If the clunk is always there when you backup(a good thing), you will only need to try a few times to verify. You might also want to have someone else back the car up while you are on the outside listening carefully for the source of the noise. In this manner it could perhaps be isolated to a specific side (and area) of the car.
If the clunk does not follow the E-brake, it could also be related to differential or connecting drive joints.